VanillaICE

This is the development version of VanillaICE; for the stable release version, see VanillaICE.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

A Hidden Markov Model for high throughput genotyping arrays

Bioconductor version: Development (3.24)

Hidden Markov Models for characterizing chromosomal alteration in high throughput SNP arrays.

Author: Robert Scharpf [aut, cre]

Maintainer: Robert Scharpf <rscharpf at jhu.edu>

Citation (from within R, enter citation("VanillaICE")):

Robert Scharpf. VanillaICE: A Hidden Markov Model for high throughput genotyping arrays. doi:10.18129/B9.bioc.VanillaICE, R package version 1.75.0, https://bioconductor.org/packages/VanillaICE.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("VanillaICE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("VanillaICE")

crlmmDownstream	PDF	R Script
VanillaICE Vignette	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, Software
Version	1.75.0
In Bioconductor since	BioC 2.1 (R-2.6) (19 years)
License	LGPL-2
Depends	R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3)
Imports	MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18
System Requirements
URL

Suggests	RUnit, human610quadv1bCrlmm
Linking To
Enhances	doMC, doMPI, doSNOW, doParallel, doRedis
Depends On Me	MinimumDistance
Imports Me
Suggests Me	oligoClasses
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	VanillaICE_1.75.0.tar.gz
Windows Binary (x86_64)	VanillaICE_1.75.0.zip
macOS Binary (big-sur-x86_64)	VanillaICE_1.75.0.tgz
macOS Binary (sonoma-arm64)	VanillaICE_1.75.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VanillaICE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VanillaICE
Package Short Url	https://bioconductor.org/packages/VanillaICE/
Package Downloads Report	Download Stats